That was it! Yay! I'll add a Trello card to have this info gem added to the docs. Thanks, Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ________________________________________ From: Aaron Petkau [aaron.petkau@gmail.com] Sent: Friday, August 01, 2014 12:26 PM To: Dooley, Damion Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Toolshed tool_dependency.xml git archive configure issue Hmmm... you know what. I tested this out and it looks like Galaxy expects the git repo to be named the same as the package name in your tool dependencies file ffp-phylogeny. If you change the git command to: git clone https://github.com/apetkau/ffp-3.19-custom.git ffp-phylogeny I think it should work. Aaron